Please note, movies and animations in the slides require Acroread
9.4.1 on Linux, or 9+ on Windows to play.

Dynamo 1.6.0 Released

DynamO 1.6.0 has been released. The major change for this release is
the switch to the CMake build system. This should make compiling on
other systems significantly simpler. The compilation tutorial has
been rewritten and now includes instructions for RedHat systems as
well as Ubuntu.

Updated: Tutorial 4 and 5 released

Two new tutorials are now available which introduce thermostats,
general data processing, compression, and multiple
Species/Interactions. Tutorial 4 also includes an introduction to
the dynatransport tool for calculating transport
properties.

Dynamo 1.5.0 Released

DynamO 1.5.0 has finally been
released. A range
of issues have been fixed (thanks to everyone who took the time
to raise issues). This version contains many major improvements,
including:

Documentation There is now a complete reference for
the output plugins and the file format. This covers almost every
feature of DynamO, but the tutorials are still being written.

Better XML error reports If there are errors in the
configuration file, you should get a much friendlier message
pointing out the location in the file where the error occurred.

More automation/Simpler configuration files Many core
features/settings required to run a system are now automatically
set up (e.g. you don't have to specify a neighbourlist, one will
be automatically set up).

Visualiser improvements The visualiser is now
capable of rendering bonds, and a range of other standard
molecular features. Shadows have also been re-enabled following a rewrite.

Better testing frameworks There is a more complete
testing system which should help prevent regressions in future
updates.

Dynamo 1.4.0 Released

DynamO 1.4.0 has finally been released. This version contains many
major improvements, including:

Automatic full checking of configuration for invalid states on
load As soon as the simulator has finished loading the
configuration, it now verifies that no particles are in an invalid
state before starting the simulation. If any particles are
"overlapping" or the capture map has become invalid, these errors
will be reported to the user on load. As these errors are the main
source of difficulty, these changes should make DynamO much easier
to use.

Fully stabilised event-detection algorithms In this
version of DynamO, all interactions have been reimplemented using
the stable EDPD approach, as detailed in
this preprint. This
greatly enhances the stability of the simulator and even allows it
to recover from some types of poorly initialised systems.

Ubuntu Packages Users using a recent ubuntu version
(12.04+) will no-longer have to compile their own copy of DynamO,
as prebuilt packages are now available at the following PPA:

New Features A few new interactions, such as
assymetric particle shapes, full wall support including
compression and polydisperse particles, and constraint forces in
gravity have been implemented.
The features gallery has been
updated with some example simulations using these features.

Changed File Format Unfortunately, the file format has
had to change to acommodate some new features and so
configurations made using DynamO v1.3 will not load in
v1.4. Although this is inconvenient for some users, at the same
time many cleanups were also implemented to ensure the file format
was as logical as possible and to maximise the
flexibility/compatibility of the format so that future upgrades
will not be so disruptive.

Rewritten Tutorials As the file format has changed,
all of the tutorials have been rewritten to reflect the changes to
the way ranges are specified. This is part of a documentation push
which will take place in the new year.

There are also a number of other minor bug fixes and
improvements. Some of which are detailed in
the Github
Issue Tracker.

Daily Ubuntu Packages Available

As part of the push to DynamO 1.4.0, a Ubuntu PPA repository has
been set up which automatically builds DynamO from the latest
development code every day.

This makes it significantly easier to get started with DynamO, as
you no longer have to compile the code yourself! To find out more,
check out the Downloads section of
the site, or click the button below.

Dynamo 1.3.2 Released

Another interim 1.3 version of DynamO is now released. There are no
major bugs fixed in this release, aside from an almost negligble
bias in the reported mean free time.

However, there are some usability fixes for the visualiser and a
great increase in the quantity of properties reported in the
simulation output file. In particular, the transport property
correlators have been completely rewritten.

Please update to either the dynamo-1-3-2 or the master branch in the
git repository.

Dynamo 1.3.1 Released

A bugfix release of DynamO is needed as there were some fairly major
bugs reported and fixed recently. Please update as soon as possible
to either the dynamo-1-3-1 or the master branch in the git
repository.

The three significant bugs fixed are as follows:

Issue
5 (major): Errors in the calculation of Cv and internal
energy on replica exchanged systems.

Dynamo 1.3 Released

The latest stable version of DynamO is now available. Thanks to a
large increase in the number of people using the code and lots of
feedback, there have been many stability fixes and general
improvements to the code base. The project now has its own website,
fully redesigned with improved documentation to encourage further
collaboration with the community.

The major new features of this release are:

New tutorials have been written to make DynamO easier to learn,
and are hosted on the new DynamO site at dynamomd.org (and .com
and .co.uk).

2D systems are now officially supported/maintained in DynamO.

Up to 50% faster in polydisperse systems.

It is now significantly easier to generate initial configurations
of dense, complex systems such as polymers.

The file format has been cleaned up to remove confusion about the
dynamics and liouvillean tags (the useless Dynamics wrapper tag
has been removed, and the Liouvillean tag has been renamed
Dynamics to make it easier for new users to understand).Configuration files created using version 1.2 will not work
with version 1.3, you will have to regenerate them.

Updated to boost 1.49.0, (you will need to do a make
distclean and make for this to take effect).

Removed the requirement for the gzip library, and switched to a
dynamic/shared version of the bzip2 library (fixes build problems
on Gentoo and Suse).

According to the git log there have been 15707 lines of code
inserted and 23107 lines of code deleted, so another big change
between versions. You can compare the changes on GitHub, but it may
take some time to display them.

This version continues the efforts to shrink and simplify the code
to make it more accessible to new developers. There are also many
bug fixes and usability improvements, all supported systems should
now work out of the box. A full changelog is posted below:

Bug fixes/Improvements

DynamO: Found the neighbourlists were not being correctly
reinitialised, causing slowdowns and possible hangs in compressing
systems (huge speed boost in compression).

DynamO: Multi-core parallel tempering is now actually in
parallel. Until now the code actually has been executing in
serial.

DynamO: Fixed a rare bug in compressing systems, where
neighbourlists would be incorrectly sized after a compression.

DynamO: Changed the default settings of the histogram
reweighting program so that the results are accurate by default!
Previously, the results coming out of dynahist_rw could be quite
innaccurate unless "--min-err=1e-16" was set.

DynamO: The uniform_01 distribution had its own copy of the
random number generator. It is unlikely that this affected any
results, but it is not good practice.

DynamO: The Green-Kubo Mutual diffusion correlator now
works (instead of just outputting NaN/inf).

Coil: Fix light placement relative to camera.

Coil: Fixed the bilateral blur filter.

Coil: Fixed many bugs which only appear when resizing the
display.

New features

Coil: Added a fullscreen mode, toggled with the f key.

Coil: Objects can now be dragged, for example, the lights
can be repositioned using the mouse.

DynamO: Packing of systems into systems is now easy to
perform.

DynamO: An estimate of the remaining time left for the
simulation is now outputted on the screen.

DynamO: Up to 50% faster in polydisperse systems thanks to
a new cache friendly nblist implementation.

DynamO: SLLOD dynamics have been removed, they are
unmaintained and unused. Shearing systems are still available
through Lees-Edwards boundary conditions, just not in transformed
co-ordinates.

DynamO: All particle positions are now shuffled for mixture
systems in dynamod to enable faster equilibration.

DynamO: Removed all deprecated Clone functions for copying
of classes in the code.

DynamO: Alter the functions in dynamics that add/get/set
objects and take/return a pointer to return shared_ptr's (search
for uses of shared_ptr's get() function).

Coil: Added new camera controls for positioning and
aligning the camera along with a new camera control modes.

Coil: Now requires and complies with the OpenGL 3.3 Core
profile.

Coil: Fixed segfaults occurring when adding a window
crashes the main render thread.

Coil: Fixed a rare segfault caused by a miscalculation of
the glade file data size stored in memory.

Coil: The snapshot button now captures using the same file
counter as the record button.

Coil: Added some sharpen and hi-pass filters to the screen
space effects.

Coil: Now it is easy to use multiple light sources in the
render scene.

Magnet: Upgraded all shaders to GLSL 330.

The next version of DynamO will focus on new features, such as
compression with walls, assymetric particle shapes, and automatic
continuous to discrete potential mapping.

New DynamO site launched

The DynamO site has been redesigned and separated from
marcusbannerman.co.uk to make it easier to find all of the information
relating to DynamO. The launch of the website is to coincide with the
release of DynamO 1.3.